Starting phenix.real_space_refine on Fri Dec 8 12:41:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb2_21585/12_2023/6wb2_21585.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb2_21585/12_2023/6wb2_21585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb2_21585/12_2023/6wb2_21585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb2_21585/12_2023/6wb2_21585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb2_21585/12_2023/6wb2_21585.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb2_21585/12_2023/6wb2_21585.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 9 5.16 5 C 5150 2.51 5 N 1465 2.21 5 O 1711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 86": "OD1" <-> "OD2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8407 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 705 Classifications: {'RNA': 33} Modifications used: {'5*END': 1, 'rna3p_pur': 19, 'rna3p_pyr': 13} Link IDs: {'rna3p': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 880 Inner-chain residues flagged as termini: ['pdbres=" G D 46 "'] Classifications: {'DNA': 4, 'RNA': 38} Modifications used: {'5*END': 2, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 41} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3854 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 504} Chain breaks: 3 Unresolved non-hydrogen bonds: 543 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 33, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 287 Chain: "B" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2968 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 30, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 12, 'GLU:plan': 29, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 210 Time building chain proxies: 5.28, per 1000 atoms: 0.63 Number of scatterers: 8407 At special positions: 0 Unit cell: (100.7, 97.52, 119.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 72 15.00 O 1711 8.00 N 1465 7.00 C 5150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 38.7% alpha, 11.4% beta 37 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.787A pdb=" N LEU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.684A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.643A pdb=" N LEU A 100 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.666A pdb=" N PHE A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.749A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 253 through 269 removed outlier: 3.533A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.534A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.582A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.763A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.695A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 6.140A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.557A pdb=" N LYS B 103 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 121 through 128 removed outlier: 4.657A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.775A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 removed outlier: 3.720A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 278 through 283 removed outlier: 4.001A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 283' Processing helix chain 'B' and resid 296 through 311 Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.979A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.513A pdb=" N TRP B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.620A pdb=" N ARG A 72 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 351 removed outlier: 7.312A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.556A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AA8, first strand: chain 'A' and resid 492 through 497 removed outlier: 4.133A pdb=" N VAL A 493 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 532 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 497 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 62 removed outlier: 3.710A pdb=" N PHE B 61 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 74 " --> pdb=" O PHE B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.586A pdb=" N VAL B 189 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR B 107 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.797A pdb=" N ILE B 132 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 354 removed outlier: 7.378A pdb=" N LYS B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN B 343 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR B 351 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR B 339 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS B 353 " --> pdb=" O TRP B 337 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TRP B 337 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 390 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2109 1.33 - 1.45: 2037 1.45 - 1.57: 4484 1.57 - 1.69: 143 1.69 - 1.80: 16 Bond restraints: 8789 Sorted by residual: bond pdb=" CA VAL A 536 " pdb=" CB VAL A 536 " ideal model delta sigma weight residual 1.537 1.549 -0.012 1.29e-02 6.01e+03 8.63e-01 bond pdb=" CA VAL A 536 " pdb=" C VAL A 536 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.05e-02 9.07e+03 5.93e-01 bond pdb=" C GLU A 432 " pdb=" N PRO A 433 " ideal model delta sigma weight residual 1.331 1.339 -0.008 1.21e-02 6.83e+03 3.88e-01 bond pdb=" CA GLU B 169 " pdb=" C GLU B 169 " ideal model delta sigma weight residual 1.520 1.528 -0.007 1.23e-02 6.61e+03 3.44e-01 bond pdb=" CA THR A 386 " pdb=" CB THR A 386 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.55e-02 4.16e+03 3.41e-01 ... (remaining 8784 not shown) Histogram of bond angle deviations from ideal: 100.80 - 107.44: 800 107.44 - 114.08: 5102 114.08 - 120.73: 3318 120.73 - 127.37: 2926 127.37 - 134.02: 261 Bond angle restraints: 12407 Sorted by residual: angle pdb=" CA LEU A 525 " pdb=" CB LEU A 525 " pdb=" CG LEU A 525 " ideal model delta sigma weight residual 116.30 124.42 -8.12 3.50e+00 8.16e-02 5.38e+00 angle pdb=" CA VAL B 35 " pdb=" CB VAL B 35 " pdb=" CG2 VAL B 35 " ideal model delta sigma weight residual 110.40 113.21 -2.81 1.70e+00 3.46e-01 2.72e+00 angle pdb=" C ILE A 37 " pdb=" N CYS A 38 " pdb=" CA CYS A 38 " ideal model delta sigma weight residual 120.31 117.97 2.34 1.52e+00 4.33e-01 2.36e+00 angle pdb=" CA LEU A 260 " pdb=" CB LEU A 260 " pdb=" CG LEU A 260 " ideal model delta sigma weight residual 116.30 121.67 -5.37 3.50e+00 8.16e-02 2.35e+00 angle pdb=" N PRO A 4 " pdb=" CA PRO A 4 " pdb=" C PRO A 4 " ideal model delta sigma weight residual 114.68 113.09 1.59 1.04e+00 9.25e-01 2.32e+00 ... (remaining 12402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 4687 16.57 - 33.13: 279 33.13 - 49.70: 96 49.70 - 66.26: 89 66.26 - 82.83: 27 Dihedral angle restraints: 5178 sinusoidal: 2424 harmonic: 2754 Sorted by residual: dihedral pdb=" O5' C D 68 " pdb=" C5' C D 68 " pdb=" C4' C D 68 " pdb=" C3' C D 68 " ideal model delta sinusoidal sigma weight residual 175.00 117.96 57.04 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" O5' C D 61 " pdb=" C5' C D 61 " pdb=" C4' C D 61 " pdb=" C3' C D 61 " ideal model delta sinusoidal sigma weight residual 55.00 111.70 -56.70 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB LYS B 70 " pdb=" CG LYS B 70 " pdb=" CD LYS B 70 " pdb=" CE LYS B 70 " ideal model delta sinusoidal sigma weight residual 60.00 112.90 -52.90 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 5175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1011 0.028 - 0.056: 282 0.056 - 0.084: 88 0.084 - 0.112: 69 0.112 - 0.141: 21 Chirality restraints: 1471 Sorted by residual: chirality pdb=" CA VAL A 536 " pdb=" N VAL A 536 " pdb=" C VAL A 536 " pdb=" CB VAL A 536 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 63 " pdb=" N ILE A 63 " pdb=" C ILE A 63 " pdb=" CB ILE A 63 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE A 50 " pdb=" N ILE A 50 " pdb=" C ILE A 50 " pdb=" CB ILE A 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1468 not shown) Planarity restraints: 1302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 278 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C GLN A 278 " 0.038 2.00e-02 2.50e+03 pdb=" O GLN A 278 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 279 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 51 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 52 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 94 " -0.022 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 95 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.019 5.00e-02 4.00e+02 ... (remaining 1299 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2438 2.81 - 3.34: 7343 3.34 - 3.86: 14475 3.86 - 4.38: 15217 4.38 - 4.90: 24135 Nonbonded interactions: 63608 Sorted by model distance: nonbonded pdb=" OG1 THR A 58 " pdb=" O ALA A 129 " model vdw 2.293 2.440 nonbonded pdb=" OG1 THR A 240 " pdb=" O VAL A 314 " model vdw 2.306 2.440 nonbonded pdb=" O GLY A 543 " pdb=" NE2 GLN A 547 " model vdw 2.324 2.520 nonbonded pdb=" OD2 ASP A 320 " pdb=" OG SER A 322 " model vdw 2.326 2.440 nonbonded pdb=" OD1 ASN A 460 " pdb=" N LYS A 461 " model vdw 2.366 2.520 ... (remaining 63603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.020 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.980 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8789 Z= 0.104 Angle : 0.443 8.118 12407 Z= 0.224 Chirality : 0.037 0.141 1471 Planarity : 0.004 0.037 1302 Dihedral : 16.015 82.830 3398 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.17 % Allowed : 4.59 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.23), residues: 932 helix: -1.60 (0.25), residues: 325 sheet: -2.38 (0.46), residues: 104 loop : -3.00 (0.23), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.000 TRP A 402 HIS 0.001 0.000 HIS B 208 PHE 0.005 0.000 PHE A 77 TYR 0.003 0.000 TYR B 115 ARG 0.001 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.2669 time to fit residues: 36.6504 Evaluate side-chains 64 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3678 time to fit residues: 1.5338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.0070 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 151 GLN A 174 GLN A 487 GLN A 494 ASN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 242 GLN B 269 GLN B 367 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8789 Z= 0.147 Angle : 0.471 5.690 12407 Z= 0.234 Chirality : 0.038 0.160 1471 Planarity : 0.004 0.048 1302 Dihedral : 16.755 76.107 2087 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.27), residues: 932 helix: 0.10 (0.30), residues: 324 sheet: -1.77 (0.46), residues: 107 loop : -2.49 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 402 HIS 0.014 0.002 HIS B 208 PHE 0.022 0.002 PHE B 171 TYR 0.021 0.001 TYR A 441 ARG 0.006 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.2034 time to fit residues: 20.6813 Evaluate side-chains 54 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 367 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN B 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8789 Z= 0.267 Angle : 0.568 9.407 12407 Z= 0.285 Chirality : 0.039 0.157 1471 Planarity : 0.004 0.051 1302 Dihedral : 16.979 80.469 2087 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.34 % Allowed : 6.29 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.27), residues: 932 helix: 0.89 (0.31), residues: 323 sheet: -1.83 (0.44), residues: 116 loop : -2.26 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 426 HIS 0.006 0.001 HIS A 361 PHE 0.012 0.002 PHE B 160 TYR 0.017 0.002 TYR A 441 ARG 0.006 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.1954 time to fit residues: 18.0322 Evaluate side-chains 41 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0822 time to fit residues: 1.3139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8789 Z= 0.129 Angle : 0.471 5.626 12407 Z= 0.233 Chirality : 0.038 0.167 1471 Planarity : 0.004 0.042 1302 Dihedral : 16.887 79.975 2087 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.28), residues: 932 helix: 1.20 (0.32), residues: 324 sheet: -1.12 (0.49), residues: 99 loop : -2.13 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.008 0.001 HIS B 208 PHE 0.006 0.001 PHE B 171 TYR 0.011 0.001 TYR A 188 ARG 0.003 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1995 time to fit residues: 18.8274 Evaluate side-chains 51 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.0020 chunk 1 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8789 Z= 0.144 Angle : 0.471 5.608 12407 Z= 0.232 Chirality : 0.038 0.142 1471 Planarity : 0.004 0.044 1302 Dihedral : 16.922 80.037 2087 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.28), residues: 932 helix: 1.30 (0.32), residues: 325 sheet: -0.87 (0.50), residues: 99 loop : -1.91 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 229 HIS 0.008 0.001 HIS B 208 PHE 0.007 0.001 PHE A 130 TYR 0.010 0.001 TYR B 115 ARG 0.003 0.001 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1988 time to fit residues: 18.8237 Evaluate side-chains 43 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8789 Z= 0.178 Angle : 0.491 6.032 12407 Z= 0.244 Chirality : 0.038 0.140 1471 Planarity : 0.004 0.042 1302 Dihedral : 17.036 81.497 2087 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.28), residues: 932 helix: 1.36 (0.32), residues: 330 sheet: -1.03 (0.47), residues: 109 loop : -1.83 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 88 HIS 0.003 0.001 HIS A 361 PHE 0.007 0.001 PHE A 87 TYR 0.019 0.001 TYR A 183 ARG 0.004 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2133 time to fit residues: 17.8794 Evaluate side-chains 44 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.0970 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8789 Z= 0.125 Angle : 0.478 5.657 12407 Z= 0.238 Chirality : 0.038 0.173 1471 Planarity : 0.003 0.038 1302 Dihedral : 16.977 79.986 2087 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.29), residues: 932 helix: 1.31 (0.32), residues: 331 sheet: -0.54 (0.50), residues: 99 loop : -1.64 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 88 HIS 0.011 0.001 HIS B 208 PHE 0.009 0.001 PHE B 160 TYR 0.018 0.001 TYR A 183 ARG 0.002 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2027 time to fit residues: 18.6046 Evaluate side-chains 45 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 0.0770 chunk 61 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 0.0870 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8789 Z= 0.147 Angle : 0.486 5.836 12407 Z= 0.241 Chirality : 0.038 0.167 1471 Planarity : 0.003 0.040 1302 Dihedral : 16.970 80.659 2087 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.29), residues: 932 helix: 1.49 (0.32), residues: 328 sheet: -0.76 (0.46), residues: 112 loop : -1.49 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 88 HIS 0.003 0.001 HIS B 208 PHE 0.024 0.001 PHE B 160 TYR 0.017 0.001 TYR A 183 ARG 0.003 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2040 time to fit residues: 17.0477 Evaluate side-chains 40 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8789 Z= 0.177 Angle : 0.506 6.347 12407 Z= 0.251 Chirality : 0.038 0.176 1471 Planarity : 0.003 0.039 1302 Dihedral : 17.042 82.396 2087 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.29), residues: 932 helix: 1.51 (0.32), residues: 328 sheet: -0.99 (0.45), residues: 118 loop : -1.41 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 88 HIS 0.008 0.001 HIS B 208 PHE 0.024 0.001 PHE B 160 TYR 0.017 0.001 TYR A 183 ARG 0.004 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2140 time to fit residues: 16.5966 Evaluate side-chains 37 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.864 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 0.0000 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8789 Z= 0.166 Angle : 0.499 5.866 12407 Z= 0.247 Chirality : 0.038 0.173 1471 Planarity : 0.004 0.039 1302 Dihedral : 17.066 82.155 2087 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.29), residues: 932 helix: 1.59 (0.32), residues: 328 sheet: -0.90 (0.46), residues: 118 loop : -1.40 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 88 HIS 0.011 0.001 HIS B 208 PHE 0.028 0.001 PHE B 160 TYR 0.018 0.001 TYR A 183 ARG 0.003 0.000 ARG B 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1932 time to fit residues: 15.6262 Evaluate side-chains 36 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.057728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.046085 restraints weight = 56637.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.047295 restraints weight = 33161.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.048134 restraints weight = 22862.240| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8789 Z= 0.123 Angle : 0.485 5.640 12407 Z= 0.238 Chirality : 0.038 0.160 1471 Planarity : 0.003 0.035 1302 Dihedral : 16.996 80.209 2087 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.29), residues: 932 helix: 1.61 (0.32), residues: 329 sheet: -0.60 (0.47), residues: 114 loop : -1.37 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 88 HIS 0.008 0.001 HIS B 208 PHE 0.029 0.001 PHE B 160 TYR 0.019 0.001 TYR A 183 ARG 0.006 0.000 ARG A 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1563.08 seconds wall clock time: 29 minutes 32.75 seconds (1772.75 seconds total)